Cairo -LRB- CNN -RRB- -- Predawn gunfire and clashes from a violent military crackdown on protesters in Cairo 's Tahrir Square on Saturday left Egyptians feeling shocked , confused and angered in the hours that followed .

Long bursts of machine-gun fire erupted overnight starting around 3 a.m. , when scores of soldiers backed by armored personnel carriers launched a raid on the square .

Amateur video posted on YouTube showed troops storming the square 's central roundabout amid rattling gunfire .

Hundreds of protesters -- calling for Egypt 's ruling military council to prosecute former president , Hosni Mubarak -- fled the scene as clouds of tear gas billowed through central Cairo . Among them were at least four wounded and bleeding men . Protesters tried to stop an ambulance from leaving the square .

Two badly beaten men in military uniform were lying in the back of the vehicle . It is not clear whether or not they were troops engaged in the crackdown -- or whether they were some of the 15 uniformed army officers and soldiers who defied direct orders by joining a protest of tens of thousands of demonstrators in Tahrir Square on Friday .

By morning , security forces withdrew from the square , leaving behind spent bullet casings and in one place , a pool of blood .

Egyptian military confirmed that one person died from a gunshot wound overnight and that 42 people were detained , including three foreigners .

`` It was a disaster , '' said protester Shadi Essam . `` The army attacked us in coordination with the police . ''

Essam said activists tried to help the dissenting military personnel to escape the crackdown by dressing four of them as civilians .

Gen. Adel Amara , a member of the Supreme Council of the Armed Forces , said security personnel did not attack the protesters .

`` Because of the pushing and clashes between the armed forces -- who I assure you had no weapons whatsoever -- because of clashes and pushing and shoving and you can imagine how a big group of protesters and soldiers could get some bruises in the pushing and shoving . Four from the armed forces -LRB- who joined the protesters -RRB- have some bruises plus nine civilian protesters , '' he said .

Tensions mounted between demonstrators and the military hours before the raid . Late Friday , activists were seen confronting two military officers who tried to approach the square 's central traffic circle . Demonstrators shoved the officers , knocking their hats off their heads , and then pursued them as they fled the square .

By daybreak , the military had withdrawn from Tahrir . Lines of barbed wire and several burned-out trucks blocked vehicle traffic from entering the area .

The clashes came a day after large crowds of protesters amassed at Tahrir Square , many of them angry with Egypt 's new military rulers . After Mubarak 's ouster in February , the military took control -- riding a wave of popularity for refusing to fire on pro-democracy protesters during 18 days of anti-government protests .

But in the weeks since , the secretive 20-man council has produced increasing frustration and criticism from different portions of the Egyptian political spectrum . Critics have complained of human rights abuses and lack of transparency in the council 's decision-making process .

On Friday , some soldiers joined the protests in a direct challenge to Egypt 's military rulers . For long intervals , they took to one of the stages erected in the crowded square and called for the country 's military rulers to be replaced .

`` If they really wanted to prosecute these corrupt officials they would have done it immediately . That 's why we are here today , '' one of the protesting officers said during the Friday protests .

Earlier this week , several military officers took to the Internet , recording video statements accusing the chairman of the ruling council , Field Marshal Mohammed Tantawi , of protecting Mubarak from prosecution and of leading a counterrevolutionary movement .

`` He should step down . He makes stupid moves . He did not learn from the mistakes of the last 60 years . Military should not run countries , '' said Mohamed Ibrahim Garib , who makes a living importing and exporting clothing , on Saturday .

Tempers flared at one point between soldiers and citizens outside the gates of the Egyptian Museum , which has been used in past months as a detainment center by the Egyptian military . An officer fired shots in the air , prompting angry youths to mob the gates and hurl stones into the museum compound . After several minutes , the confrontation subsided .

The military issued a communique Saturday morning , accusing a former member of Hosni Mubarak 's long-ruling National Democratic Party of `` inciting people in Tahrir . ''

The military announced it had issued arrest warrants for NDP member Ibrahim Kamel and several of his associates , after accusing them of being `` present in Tahrir Square after curfew as thugs and scaring the citizens . ''

In scenes reminiscent of street protests last January and February , activists have once again blocked entry into Tahrir , using coils of barbed wire apparently left behind by the military .

CNN 's Ivan Watson and Mohamed Fadel Fahmy contributed to this report

@highlight

NEW : One person dies from a gunshot wound and 42 people are detained

@highlight

Military launches predawn raid on Tahrir protesters

@highlight

The demonstrators are seeking the prosecution of former President Hosni Mubarak

@highlight

They are also unhappy with the military 's secretive 20-man council